Genomic Location: NW_027103553.1:109...39659
NR annotation: XP_047123873.1, E3 ubiquitin-protein ligase HERC2 isoform X1 [Hydra vulgaris]
Species Clytia hemisphaerica · all data for this species · gene families
| CDS |
| XP_066913164.1 |
| Protein |
| XP_066913164.1 |
| UniProt accession | Description |
|---|---|
| O95714 | E3 ubiquitin-protein ligase HERC2 OS=Homo sapiens OX=9606 GN=HERC2 PE=1 SV=2 |
| Q4U2R1 | E3 ubiquitin-protein ligase HERC2 OS=Mus musculus OX=10090 GN=Herc2 PE=1 SV=3 |
| Q9VR91 | Probable E3 ubiquitin-protein ligase HERC2 OS=Drosophila melanogaster OX=7227 GN=HERC2 PE=1 SV=3 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0002592 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF00569 all species → | ZZ | Zinc finger, ZZ type | Domain | Interproscan |
| PF06701 all species → | MIB_HERC2 | Mib_herc2 | Domain | Interproscan |
| PF13540 all species → | RCC1_2 | Regulator of chromosome condensation (RCC1) repeat | Repeat | Interproscan |
| PF00415 all species → | RCC1 | Regulator of chromosome condensation (RCC1) repeat | Repeat | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR000433 all species → | Domain | Zinc finger, ZZ-type | Interproscan |
| IPR009091 all species → | Homologous_superfamily | Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II | Interproscan |
| IPR008979 all species → | Homologous_superfamily | Galactose-binding-like domain superfamily | Interproscan |
| IPR000408 all species → | Repeat | Regulator of chromosome condensation, RCC1 | Interproscan |
| IPR051210 all species → | Family | Ubiquitin ligases and GEF domain-containing protein | Interproscan |
| IPR037252 all species → | Homologous_superfamily | Mib/herc2 domain superfamily | Interproscan |
| IPR010606 all species → | Domain | Mib-herc2 | Interproscan |
| IPR015940 all species → | Domain | Ubiquitin-associated domain | Interproscan |
| IPR043145 all species → | Homologous_superfamily | Zinc finger, ZZ-type superfamily | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR22870 all species → | REGULATOR OF CHROMOSOME CONDENSATION | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0008270 all species → | Molecular Function | zinc ion binding | Interproscan |
| GO:0004842 all species → | Molecular Function | ubiquitin-protein transferase activity | Interproscan |
| GO:0046872 all species → | Molecular Function | metal ion binding | Interproscan |
| GO:0016567 all species → | Biological Process | protein ubiquitination | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K10595 | HERC2; E3 ubiquitin-protein ligase HERC2 | EC:2.3.2.26 | DNA repair and recombination proteins | ko03400 | deepkoala |
Transcript abundance of XP_066913164.1 across 40 RNA-seq samples of Clytia hemisphaerica. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.
| Condition | Samples | TPM > 0 | Mean TPM | Max TPM | Mean, relative to max |
|---|---|---|---|---|---|
| Mature medusa | 5 | 5 | 5.46 | 12.72 | |
| medusa · Experiment Condition A1 | 4 | 4 | 5.17 | 5.51 | |
| medusa · Experiment Condition A2 | 4 | 4 | 6.26 | 7.01 | |
| medusa · Experiment Condition A3 | 4 | 4 | 12.08 | 12.88 | |
| Early gastrula | 2 | 2 | 4.54 | 4.91 | |
| Planula 24hpf | 2 | 2 | 4.25 | 4.82 | |
| Planula 48hpf | 2 | 2 | 2.44 | 2.46 | |
| Planula 72hpf | 2 | 2 | 3.09 | 3.12 | |
| Primary polyp | 2 | 2 | 3.63 | 3.78 | |
| Gastrozooid | 2 | 2 | 4.18 | 4.71 | |
| Gonozooid | 2 | 2 | 3.81 | 4.07 | |
| Stolon | 2 | 2 | 3.79 | 4.40 | |
| Baby medusa | 2 | 2 | 5.91 | 6.01 | |
| medusa · Experiment Condition B1 | 2 | 2 | 6.02 | 6.20 | |
| medusa · Experiment Condition B2 | 2 | 2 | 4.54 | 4.65 | |
| Mixed | 1 | 1 | 4.09 | 4.09 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| ERR2862245 | Mature medusa | not recorded | Mature medusa | not recorded | ERP110164 | 12.72 |
| ERR2816251 | Mature medusa | not recorded | Mature medusa | not recorded | ERP110164 | 5.26 |
| ERR2816249 | Mature medusa | not recorded | Mature medusa | not recorded | ERP110164 | 4.04 |
| ERR2816250 | Mature medusa | not recorded | Mature medusa | not recorded | ERP110164 | 2.76 |
| ERR2816248 | Mature medusa | not recorded | Mature medusa | not recorded | ERP110164 | 2.52 |
| ERR3299477 | medusa · Experiment Condition A1 | not recorded | medusa | Experiment Condition A1 | ERP115020 | 5.51 |
| ERR3299476 | medusa · Experiment Condition A1 | not recorded | medusa | Experiment Condition A1 | ERP115020 | 5.38 |
| ERR3299475 | medusa · Experiment Condition A1 | not recorded | medusa | Experiment Condition A1 | ERP115020 | 5.06 |
| ERR3299478 | medusa · Experiment Condition A1 | not recorded | medusa | Experiment Condition A1 | ERP115020 | 4.74 |
| ERR3299482 | medusa · Experiment Condition A2 | not recorded | medusa | Experiment Condition A2 | ERP115020 | 7.01 |
| ERR3299481 | medusa · Experiment Condition A2 | not recorded | medusa | Experiment Condition A2 | ERP115020 | 6.67 |
| ERR3299480 | medusa · Experiment Condition A2 | not recorded | medusa | Experiment Condition A2 | ERP115020 | 5.73 |
| ERR3299479 | medusa · Experiment Condition A2 | not recorded | medusa | Experiment Condition A2 | ERP115020 | 5.62 |
| ERR3299486 | medusa · Experiment Condition A3 | not recorded | medusa | Experiment Condition A3 | ERP115020 | 12.88 |
| ERR3299483 | medusa · Experiment Condition A3 | not recorded | medusa | Experiment Condition A3 | ERP115020 | 11.96 |
| ERR3299485 | medusa · Experiment Condition A3 | not recorded | medusa | Experiment Condition A3 | ERP115020 | 11.95 |
| ERR3299484 | medusa · Experiment Condition A3 | not recorded | medusa | Experiment Condition A3 | ERP115020 | 11.53 |
| ERR2816230 | Early gastrula | not recorded | Early gastrula | not recorded | ERP110164 | 4.91 |
| ERR2816231 | Early gastrula | not recorded | Early gastrula | not recorded | ERP110164 | 4.16 |
| ERR2816233 | Planula 24hpf | not recorded | Planula 24hpf | not recorded | ERP110164 | 4.82 |
| ERR2816232 | Planula 24hpf | not recorded | Planula 24hpf | not recorded | ERP110164 | 3.68 |
| ERR2816234 | Planula 48hpf | not recorded | Planula 48hpf | not recorded | ERP110164 | 2.46 |
| ERR2816235 | Planula 48hpf | not recorded | Planula 48hpf | not recorded | ERP110164 | 2.42 |
| ERR2816237 | Planula 72hpf | not recorded | Planula 72hpf | not recorded | ERP110164 | 3.12 |
| ERR2816236 | Planula 72hpf | not recorded | Planula 72hpf | not recorded | ERP110164 | 3.06 |
| ERR2816239 | Primary polyp | not recorded | Primary polyp | not recorded | ERP110164 | 3.78 |
| ERR2816238 | Primary polyp | not recorded | Primary polyp | not recorded | ERP110164 | 3.48 |
| ERR2816241 | Gastrozooid | not recorded | Gastrozooid | not recorded | ERP110164 | 4.71 |
| ERR2816240 | Gastrozooid | not recorded | Gastrozooid | not recorded | ERP110164 | 3.65 |
| ERR2816243 | Gonozooid | not recorded | Gonozooid | not recorded | ERP110164 | 4.07 |
| ERR2816242 | Gonozooid | not recorded | Gonozooid | not recorded | ERP110164 | 3.55 |
| ERR2816245 | Stolon | not recorded | Stolon | not recorded | ERP110164 | 4.40 |
| ERR2816244 | Stolon | not recorded | Stolon | not recorded | ERP110164 | 3.17 |
| ERR2816247 | Baby medusa | not recorded | Baby medusa | not recorded | ERP110164 | 6.01 |
| ERR2816246 | Baby medusa | not recorded | Baby medusa | not recorded | ERP110164 | 5.81 |
| ERR3299471 | medusa · Experiment Condition B1 | not recorded | medusa | Experiment Condition B1 | ERP115020 | 6.20 |
| ERR3299472 | medusa · Experiment Condition B1 | not recorded | medusa | Experiment Condition B1 | ERP115020 | 5.83 |
| ERR3299473 | medusa · Experiment Condition B2 | not recorded | medusa | Experiment Condition B2 | ERP115020 | 4.65 |
| ERR3299474 | medusa · Experiment Condition B2 | not recorded | medusa | Experiment Condition B2 | ERP115020 | 4.42 |
| ERR2862244 | Mixed | not recorded | Mixed | not recorded | ERP110164 | 4.09 |
Source: CnidoSite RNA-seq expression matrices (CHEMI_TPM,
StringTie quantification over 40 runs), joined to SRA sample
metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped
by the descriptor carried in the expression matrix itself.
Genes whose expression across the transcriptome samples of Clytia hemisphaerica tracks this one. Counts are over the whole network; the network view itself draws at most 100 partners per query gene (CNIDO_NET_TOP_K), so a hub gene can show fewer edges than the number below.
| Direction | Partners | Most correlated partner | PCC |
|---|---|---|---|
| Positively correlated | 24 | XP_066921715.1 | 0.943503166437393 |
| Negatively correlated | 10 | XP_066923370.1 | -0.829646764726956 |
Open this gene in Network Analysis → The network opens with the gene already entered and both directions selected. There you can add up to 9 more genes, switch between the positive and negative network, and export the edge list.
Whether this gene can be visualised in the single-cell atlases of Clytia hemisphaerica, and in which cell types it is a marker. Expression is stored per cell, so the violin plot and the cell-type means are computed in the viewer — open a dataset to see them.
No single-cell dataset has been published for this species. The atlases that do exist are listed in the Cell Atlas.
Chromatin and DNA-methylation data covering this gene. Peak calls are listed per sample with the genomic region the peak falls in; DNA methylation is listed as sample availability only, because those tables are queried by the DNA Methylation page itself.
No epigenomic data has been deposited for this species. The assays that exist across the site are described in the Epigenomic Data module.
Every tool below opens with this gene already entered, so you land on the analysis rather than on an empty form. Links open in a new tab.
| Analysis | What it does | Status | |
|---|---|---|---|
| Primer design | Design PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed. | template found | open → |
| BLAST | Search this gene’s sequence against the CnidoSite BLAST databases. The query is filled in and the species’ database is preselected — press Run to start. | template found | open → |
| Expression heatmap | Draw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it. | ready | open → |
| Gene family / orthogroup | Look this gene up in the single-copy orthogroups built from the high-quality cnidarian genomes, and see which other species carry an orthologue. | open → | |
| Gene set analysis | Start a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it. | open → |
